This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Numerous large multidimensional datasets communicating the relationships between individual proteins and protein superfamilies have been collected by experimental means. Extracting relevant information from these datasets through qualitative and quantitative analysis has proven difficult. Cytoscape, an open source Web-based application developed for the purposes of visualizing and analyzing protein-protein networks, could serve as a useful tool for studying these datasets. Our goal is to develop new "plug-ins" for Cytoscape that will allow researchers to visually and quantitatively understand experimentally determined associations between protein superfamilies. Potentially, we would like to couple Cytoscape with structural analysis software to provide even more powerful means of investigating large protein superfamily datasets.